Structure of PDB 8cdv Chain C Binding Site BS01

Receptor Information
>8cdv Chain C (length=457) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEAFMEKLLSFMKEEAYKPLTVQELEEMLNITEAEEFKELVKALVALEEK
GLIVRTRSDRYGIPEKMADAMEQASSTPDTIDEKDLKDRRDLRDQVIVTI
DGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPIDKEALERGT
SVYLVDRVIPMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQVTEHEIF
QSVIKTTERMTYSDVNKILVDDDEELKQKYEPLVPMFKDMERLAQILRDK
RMDRGAVDFDFKEAKVLVDDEGAVKDVVIRERSVAEKLIEEFMLVANETV
AEHFHWMNVPFIYRIHEEPNAEKLQKFLEFVTTFGYVVKGTAGNIHPRAL
QSILDAVRDRPEETVISTVMLRSMKQAKYDPQSLGHFGLSTEFYTHFTSP
IRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHTSSMERRAVD
AERETDD
Ligand information
>8cdv Chain A (length=1247) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggagaguuugauccuggcucaggacgaacgcuggcggcgugccuaauaca
ugcaagucgagcggacagauguuagcggcggacgggugaguaacacgugg
guaaccugccuguaagacugggauaacuccgggaaaccggggcuaauacc
ggaugguuguuugaaccgcaugguucaaacauaaaagguggcuucggcua
ccacuuacagauggacccgcggcgcauuagcuaguuggugagguaacggc
ucaccaaggcgacgaugcguagccgaccugagagggugaucggccacacu
gggacugagacacggcccagacuccuacgggaggcagcaguagggaaucu
uccgcaauggacgaaagucugacggagcaacgccgcgugagugaugaagg
uuuucggaucguaaagcucuguuguuagggaagaacaagugccguucgaa
uagggcgguaccuugacgguaccuaaccagaaagccacggcuaacuacgu
gccagcagccgcgguaauacguagguggcaagcguuguccggaauuauug
ggcguaaagggcucgcaggcgguuucuuaagucugaugugaaagcccccg
gcucaaccggggagggucauuggaaacuggggaacuugagugcagaagag
gagaguggaauuccacguguagcggugaaaugcguagagauguggaggaa
caccaguggcgaaggcgacucucuggucuguaacugacgcugaggagcga
aagcgugggcacgccguaaacgaugagugcuaaguguuaggggguuuccg
ccccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacgg
ucgcaagacugaaacucaaaggaauugaguggagcaugugguuuaauucg
aagcaacgcgaagaaccuuaccaggucuugacauccucugacaauccuag
agauaggacguccccuucgggggcagagugacagcgcaacccuugaucuu
aguugccagcauucaguugggcacucuaaggugacugccggugacaaacc
ggaggaagguggggaugacgucaaaucaucaugccccuuaugaccugggc
uacacacgugcuacaauggacagaacaaagggcagcgaaaccgcgagguu
aagccaaucccacaaaucuguucucaguucggaucgcagucugcaacucg
acugcgugaagcuggaaucgcuaguaaucgcggaucagcaugccgcg
...<<<<....((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<<.
<<<..<<<..<<.<........>.>>>>>......<<........<<<<<
<<..<<...<<<<<<<..<<<.....<<<<<<....>>>>>>......>>
>......<<<<<<<<<<....>>>>>>>>>>.....<<<<<<<..>>>>>
>>.>>>>>>>..>>>>>>>>>.<<<....<<<..<<<<<<<<.......>
>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<
<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>.......
.<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<
<<....>>>>.....>>>>....<<<<<<.......<.<<<<<<<<<...
..>>>>>>>>>.>........>>>>>>......<<<<<(((...<<<<<.
....<<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........
<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<.......<<<<<
<.....>>>>>>.....>>>>>>>..>>>>>>>>>...<<<<<<<<...<
<<<<<<....<.<<.......<<<......>>>..........>>.>...
........<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>..
..<<<<<..>>>>>..........<<<<<<..<<<<<<<<<<<<......
>>>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.<<<.......<
<<....>>>.....>>>..))))......<..<<<<<<<<..........
....................<<<<<<<........<<.......<<<<<.
...>>>>>.....<<....>>.....>>.............<....<<<<
.....<....<.....>..>.......>>>>......<<<<<.....>>>
>>.........>.............................>>>>>>>..
....>>>>>>>>.....<<<<<<<.....<<<..<<..<.........>.
..>>....>>>.....>>>>>>>...........<<<<<<<........>
>>>>>>.........>............<<<<<.........>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8cdv Structural basis of ribosomal 30S subunit degradation by RNase R
Resolution4.73 Å
Binding residue
(original residue number in PDB)		K40 W465 N503
Binding residue
(residue number reindexed from 1)		K38 W306 N344
Enzymatic activity
Enzyme Commision number 3.1.13.1: exoribonuclease II.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0008859 exoribonuclease II activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0016070 RNA metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cdv, PDBe:8cdv, PDBj:8cdv
PDBsum8cdv
PubMed38326618
UniProtO32231|RNR_BACSU Ribonuclease R (Gene Name=rnr)

[Back to BioLiP]